Starting phenix.real_space_refine on Tue Sep 15 08:59:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pus_20480/09_2026/6pus_20480.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pus_20480/09_2026/6pus_20480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pus_20480/09_2026/6pus_20480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pus_20480/09_2026/6pus_20480.map" model { file = "/net/cci-nas-00/data/ceres_data/6pus_20480/09_2026/6pus_20480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pus_20480/09_2026/6pus_20480.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pus_20480/09_2026/6pus_20480.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pus_20480/09_2026/6pus_20480.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 16 5.49 5 S 140 5.16 5 C 24148 2.51 5 N 6640 2.21 5 O 6432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.16s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37380 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1306, 9272 Classifications: {'peptide': 1306} Incomplete info: {'truncation_to_alanine': 356} Link IDs: {'PTRANS': 62, 'TRANS': 1243} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1310 Unresolved non-hydrogen angles: 1654 Unresolved non-hydrogen dihedrals: 1073 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 25, 'GLU:plan': 63, 'PHE:plan': 12, 'ASP:plan': 43, 'HIS:plan': 14, 'TRP:plan': 5, 'ASN:plan1': 11, 'ARG:plan': 23, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 858 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {' CA': 1, 'APR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, D, B Time building chain proxies: 13.29, per 1000 atoms: 0.36 Number of scatterers: 37380 At special positions: 0 Unit cell: (157.878, 157.878, 165.396, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 140 16.00 P 16 15.00 O 6432 8.00 N 6640 7.00 C 24148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.9 seconds 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9856 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 32 sheets defined 55.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 56 through 67 removed outlier: 3.756A pdb=" N SER A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.693A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.661A pdb=" N ILE A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 3.752A pdb=" N LYS A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.553A pdb=" N LYS A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.628A pdb=" N HIS A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 365 Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.695A pdb=" N ILE A 374 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 387 removed outlier: 3.761A pdb=" N VAL A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 395 through 412 removed outlier: 4.320A pdb=" N ARG A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 445 removed outlier: 3.739A pdb=" N GLN A 435 " --> pdb=" O VAL A 431 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 462 removed outlier: 3.905A pdb=" N LEU A 456 " --> pdb=" O TRP A 452 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 458 " --> pdb=" O HIS A 454 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.502A pdb=" N ALA A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 483 Processing helix chain 'A' and resid 484 through 494 removed outlier: 3.731A pdb=" N ALA A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 removed outlier: 3.662A pdb=" N VAL A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.542A pdb=" N ASN A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 542 removed outlier: 3.763A pdb=" N SER A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.810A pdb=" N VAL A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 removed outlier: 4.168A pdb=" N ASP A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN A 632 " --> pdb=" O TRP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 642 removed outlier: 3.507A pdb=" N ALA A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.562A pdb=" N LEU A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 659 " --> pdb=" O CYS A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 697 removed outlier: 3.890A pdb=" N GLU A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 679 " --> pdb=" O MET A 675 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 695 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 697 " --> pdb=" O CYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 717 through 724 Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.519A pdb=" N SER A 731 " --> pdb=" O MET A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 744 Processing helix chain 'A' and resid 753 through 762 Processing helix chain 'A' and resid 762 through 768 removed outlier: 4.236A pdb=" N LEU A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 767 " --> pdb=" O PHE A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 783 through 794 removed outlier: 3.858A pdb=" N ALA A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 819 removed outlier: 3.606A pdb=" N VAL A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 849 removed outlier: 3.659A pdb=" N CYS A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 832 " --> pdb=" O CYS A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 866 through 888 Processing helix chain 'A' and resid 891 through 912 removed outlier: 3.636A pdb=" N VAL A 897 " --> pdb=" O TYR A 893 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 908 " --> pdb=" O ILE A 904 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 916 Processing helix chain 'A' and resid 920 through 956 removed outlier: 3.880A pdb=" N ILE A 926 " --> pdb=" O PRO A 922 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP A 933 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 980 removed outlier: 3.520A pdb=" N GLY A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1036 Processing helix chain 'A' and resid 1038 through 1056 removed outlier: 3.791A pdb=" N GLN A1054 " --> pdb=" O TYR A1050 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN A1056 " --> pdb=" O PHE A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1067 Processing helix chain 'A' and resid 1067 through 1077 removed outlier: 3.875A pdb=" N ILE A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1099 removed outlier: 3.915A pdb=" N SER A1088 " --> pdb=" O PHE A1084 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1141 removed outlier: 3.718A pdb=" N ALA A1120 " --> pdb=" O ASN A1116 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A1131 " --> pdb=" O TYR A1127 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A1134 " --> pdb=" O GLU A1130 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1165 removed outlier: 3.657A pdb=" N ASP A1165 " --> pdb=" O LEU A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1282 removed outlier: 4.070A pdb=" N ASP A1282 " --> pdb=" O GLU A1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1279 through 1282' Processing helix chain 'A' and resid 1288 through 1292 removed outlier: 3.951A pdb=" N ASP A1291 " --> pdb=" O PRO A1288 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A1292 " --> pdb=" O MET A1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1288 through 1292' Processing helix chain 'A' and resid 1397 through 1404 Processing helix chain 'A' and resid 1410 through 1418 Processing helix chain 'A' and resid 1455 through 1463 removed outlier: 3.835A pdb=" N ARG A1459 " --> pdb=" O VAL A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1496 removed outlier: 3.512A pdb=" N LEU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 67 Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.692A pdb=" N ILE C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 202 removed outlier: 3.661A pdb=" N ILE C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C 194 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 229 removed outlier: 3.752A pdb=" N LYS C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 Processing helix chain 'C' and resid 298 through 312 removed outlier: 3.552A pdb=" N LYS C 307 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 312 " --> pdb=" O PHE C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.628A pdb=" N HIS C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C 345 " --> pdb=" O ASP C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 365 Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.695A pdb=" N ILE C 374 " --> pdb=" O VAL C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 387 removed outlier: 3.761A pdb=" N VAL C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 395 through 412 removed outlier: 4.320A pdb=" N ARG C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 445 removed outlier: 3.740A pdb=" N GLN C 435 " --> pdb=" O VAL C 431 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 462 removed outlier: 3.905A pdb=" N LEU C 456 " --> pdb=" O TRP C 452 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 457 " --> pdb=" O ASP C 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 458 " --> pdb=" O HIS C 454 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.503A pdb=" N ALA C 468 " --> pdb=" O ARG C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 483 Processing helix chain 'C' and resid 484 through 494 removed outlier: 3.732A pdb=" N ALA C 491 " --> pdb=" O THR C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 507 removed outlier: 3.662A pdb=" N VAL C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 514 Processing helix chain 'C' and resid 515 through 525 removed outlier: 3.541A pdb=" N ASN C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 542 removed outlier: 3.763A pdb=" N SER C 534 " --> pdb=" O CYS C 530 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU C 542 " --> pdb=" O LYS C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 570 removed outlier: 3.810A pdb=" N VAL C 561 " --> pdb=" O GLN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 632 removed outlier: 4.168A pdb=" N ASP C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 642 removed outlier: 3.507A pdb=" N ALA C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 663 removed outlier: 3.562A pdb=" N LEU C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 659 " --> pdb=" O CYS C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 697 removed outlier: 3.890A pdb=" N GLU C 674 " --> pdb=" O ASP C 670 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 679 " --> pdb=" O MET C 675 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 695 " --> pdb=" O THR C 691 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP C 697 " --> pdb=" O CYS C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 702 Processing helix chain 'C' and resid 703 through 705 No H-bonds generated for 'chain 'C' and resid 703 through 705' Processing helix chain 'C' and resid 717 through 724 Processing helix chain 'C' and resid 726 through 731 removed outlier: 3.519A pdb=" N SER C 731 " --> pdb=" O MET C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 744 Processing helix chain 'C' and resid 753 through 762 Processing helix chain 'C' and resid 762 through 768 removed outlier: 4.236A pdb=" N LEU C 766 " --> pdb=" O ALA C 762 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 767 " --> pdb=" O PHE C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 781 Processing helix chain 'C' and resid 783 through 794 removed outlier: 3.858A pdb=" N ALA C 794 " --> pdb=" O ALA C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 819 removed outlier: 3.607A pdb=" N VAL C 819 " --> pdb=" O TYR C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 849 removed outlier: 3.659A pdb=" N CYS C 830 " --> pdb=" O SER C 826 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 832 " --> pdb=" O CYS C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 865 Processing helix chain 'C' and resid 866 through 888 Processing helix chain 'C' and resid 891 through 912 removed outlier: 3.636A pdb=" N VAL C 897 " --> pdb=" O TYR C 893 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 903 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 908 " --> pdb=" O ILE C 904 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS C 912 " --> pdb=" O LEU C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 916 Processing helix chain 'C' and resid 920 through 956 removed outlier: 3.881A pdb=" N ILE C 926 " --> pdb=" O PRO C 922 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 940 " --> pdb=" O PHE C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 980 removed outlier: 3.520A pdb=" N GLY C 980 " --> pdb=" O LEU C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1036 Processing helix chain 'C' and resid 1038 through 1056 removed outlier: 3.791A pdb=" N GLN C1054 " --> pdb=" O TYR C1050 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN C1056 " --> pdb=" O PHE C1052 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1067 Processing helix chain 'C' and resid 1067 through 1077 removed outlier: 3.875A pdb=" N ILE C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1084 through 1099 removed outlier: 3.916A pdb=" N SER C1088 " --> pdb=" O PHE C1084 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN C1091 " --> pdb=" O LEU C1087 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1141 removed outlier: 3.718A pdb=" N ALA C1120 " --> pdb=" O ASN C1116 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU C1130 " --> pdb=" O ILE C1126 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN C1131 " --> pdb=" O TYR C1127 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C1134 " --> pdb=" O GLU C1130 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN C1135 " --> pdb=" O ASN C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1165 removed outlier: 3.657A pdb=" N ASP C1165 " --> pdb=" O LEU C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1282 removed outlier: 4.070A pdb=" N ASP C1282 " --> pdb=" O GLU C1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1279 through 1282' Processing helix chain 'C' and resid 1288 through 1292 removed outlier: 3.951A pdb=" N ASP C1291 " --> pdb=" O PRO C1288 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C1292 " --> pdb=" O MET C1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1288 through 1292' Processing helix chain 'C' and resid 1397 through 1404 Processing helix chain 'C' and resid 1410 through 1418 Processing helix chain 'C' and resid 1455 through 1463 removed outlier: 3.835A pdb=" N ARG C1459 " --> pdb=" O VAL C1455 " (cutoff:3.500A) Processing helix chain 'C' and resid 1485 through 1496 removed outlier: 3.512A pdb=" N LEU C1491 " --> pdb=" O ASN C1487 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 67 Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.693A pdb=" N ILE D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 202 removed outlier: 3.661A pdb=" N ILE D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 194 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY D 202 " --> pdb=" O ALA D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 229 removed outlier: 3.753A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER D 226 " --> pdb=" O VAL D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 298 through 312 removed outlier: 3.553A pdb=" N LYS D 307 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 308 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN D 312 " --> pdb=" O PHE D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.628A pdb=" N HIS D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D 345 " --> pdb=" O ASP D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 365 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.695A pdb=" N ILE D 374 " --> pdb=" O VAL D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 387 removed outlier: 3.761A pdb=" N VAL D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 Processing helix chain 'D' and resid 395 through 412 removed outlier: 4.320A pdb=" N ARG D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 445 removed outlier: 3.739A pdb=" N GLN D 435 " --> pdb=" O VAL D 431 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 462 removed outlier: 3.906A pdb=" N LEU D 456 " --> pdb=" O TRP D 452 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 457 " --> pdb=" O ASP D 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 458 " --> pdb=" O HIS D 454 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 471 removed outlier: 3.503A pdb=" N ALA D 468 " --> pdb=" O ARG D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 483 Processing helix chain 'D' and resid 484 through 494 removed outlier: 3.731A pdb=" N ALA D 491 " --> pdb=" O THR D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 507 removed outlier: 3.662A pdb=" N VAL D 500 " --> pdb=" O LYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 Processing helix chain 'D' and resid 515 through 525 removed outlier: 3.542A pdb=" N ASN D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 542 removed outlier: 3.763A pdb=" N SER D 534 " --> pdb=" O CYS D 530 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU D 542 " --> pdb=" O LYS D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 570 removed outlier: 3.810A pdb=" N VAL D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 632 removed outlier: 4.168A pdb=" N ASP D 624 " --> pdb=" O ASP D 620 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN D 632 " --> pdb=" O TRP D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 642 removed outlier: 3.508A pdb=" N ALA D 638 " --> pdb=" O ARG D 634 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 663 removed outlier: 3.563A pdb=" N LEU D 653 " --> pdb=" O ILE D 649 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 659 " --> pdb=" O CYS D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 697 removed outlier: 3.891A pdb=" N GLU D 674 " --> pdb=" O ASP D 670 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA D 679 " --> pdb=" O MET D 675 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU D 692 " --> pdb=" O GLY D 688 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 695 " --> pdb=" O THR D 691 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP D 697 " --> pdb=" O CYS D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 702 Processing helix chain 'D' and resid 703 through 705 No H-bonds generated for 'chain 'D' and resid 703 through 705' Processing helix chain 'D' and resid 717 through 724 Processing helix chain 'D' and resid 726 through 731 removed outlier: 3.519A pdb=" N SER D 731 " --> pdb=" O MET D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 744 Processing helix chain 'D' and resid 753 through 762 Processing helix chain 'D' and resid 762 through 768 removed outlier: 4.236A pdb=" N LEU D 766 " --> pdb=" O ALA D 762 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU D 767 " --> pdb=" O PHE D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 781 Processing helix chain 'D' and resid 783 through 794 removed outlier: 3.857A pdb=" N ALA D 794 " --> pdb=" O ALA D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 819 removed outlier: 3.606A pdb=" N VAL D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 849 removed outlier: 3.659A pdb=" N CYS D 830 " --> pdb=" O SER D 826 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 832 " --> pdb=" O CYS D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 865 Processing helix chain 'D' and resid 866 through 888 Processing helix chain 'D' and resid 891 through 912 removed outlier: 3.636A pdb=" N VAL D 897 " --> pdb=" O TYR D 893 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE D 903 " --> pdb=" O LEU D 899 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 908 " --> pdb=" O ILE D 904 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D 911 " --> pdb=" O CYS D 907 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS D 912 " --> pdb=" O LEU D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 916 Processing helix chain 'D' and resid 920 through 956 removed outlier: 3.880A pdb=" N ILE D 926 " --> pdb=" O PRO D 922 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP D 933 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE D 936 " --> pdb=" O LYS D 932 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 940 " --> pdb=" O PHE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 980 removed outlier: 3.520A pdb=" N GLY D 980 " --> pdb=" O LEU D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1036 Processing helix chain 'D' and resid 1038 through 1056 removed outlier: 3.791A pdb=" N GLN D1054 " --> pdb=" O TYR D1050 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN D1056 " --> pdb=" O PHE D1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1067 Processing helix chain 'D' and resid 1067 through 1077 removed outlier: 3.875A pdb=" N ILE D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1099 removed outlier: 3.915A pdb=" N SER D1088 " --> pdb=" O PHE D1084 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN D1091 " --> pdb=" O LEU D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1141 removed outlier: 3.718A pdb=" N ALA D1120 " --> pdb=" O ASN D1116 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU D1130 " --> pdb=" O ILE D1126 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN D1131 " --> pdb=" O TYR D1127 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN D1134 " --> pdb=" O GLU D1130 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN D1135 " --> pdb=" O ASN D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1165 removed outlier: 3.657A pdb=" N ASP D1165 " --> pdb=" O LEU D1161 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1282 removed outlier: 4.070A pdb=" N ASP D1282 " --> pdb=" O GLU D1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1279 through 1282' Processing helix chain 'D' and resid 1288 through 1292 removed outlier: 3.951A pdb=" N ASP D1291 " --> pdb=" O PRO D1288 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D1292 " --> pdb=" O MET D1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1288 through 1292' Processing helix chain 'D' and resid 1397 through 1404 Processing helix chain 'D' and resid 1410 through 1418 Processing helix chain 'D' and resid 1455 through 1463 removed outlier: 3.835A pdb=" N ARG D1459 " --> pdb=" O VAL D1455 " (cutoff:3.500A) Processing helix chain 'D' and resid 1485 through 1496 removed outlier: 3.511A pdb=" N LEU D1491 " --> pdb=" O ASN D1487 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 67 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.693A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.662A pdb=" N ILE B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 194 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 removed outlier: 3.752A pdb=" N LYS B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 298 through 312 removed outlier: 3.553A pdb=" N LYS B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.628A pdb=" N HIS B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 365 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.695A pdb=" N ILE B 374 " --> pdb=" O VAL B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 387 removed outlier: 3.761A pdb=" N VAL B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 395 through 412 removed outlier: 4.320A pdb=" N ARG B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 445 removed outlier: 3.738A pdb=" N GLN B 435 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 462 removed outlier: 3.905A pdb=" N LEU B 456 " --> pdb=" O TRP B 452 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 457 " --> pdb=" O ASP B 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 458 " --> pdb=" O HIS B 454 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.502A pdb=" N ALA B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 483 Processing helix chain 'B' and resid 484 through 494 removed outlier: 3.731A pdb=" N ALA B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 507 removed outlier: 3.662A pdb=" N VAL B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 515 through 525 removed outlier: 3.542A pdb=" N ASN B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 542 removed outlier: 3.762A pdb=" N SER B 534 " --> pdb=" O CYS B 530 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 570 removed outlier: 3.810A pdb=" N VAL B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 632 removed outlier: 4.168A pdb=" N ASP B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 642 removed outlier: 3.507A pdb=" N ALA B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 663 removed outlier: 3.562A pdb=" N LEU B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 659 " --> pdb=" O CYS B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 697 removed outlier: 3.890A pdb=" N GLU B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 695 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 697 " --> pdb=" O CYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'B' and resid 703 through 705 No H-bonds generated for 'chain 'B' and resid 703 through 705' Processing helix chain 'B' and resid 717 through 724 Processing helix chain 'B' and resid 726 through 731 removed outlier: 3.519A pdb=" N SER B 731 " --> pdb=" O MET B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 744 Processing helix chain 'B' and resid 753 through 762 Processing helix chain 'B' and resid 762 through 768 removed outlier: 4.237A pdb=" N LEU B 766 " --> pdb=" O ALA B 762 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 767 " --> pdb=" O PHE B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 783 through 794 removed outlier: 3.858A pdb=" N ALA B 794 " --> pdb=" O ALA B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 819 removed outlier: 3.606A pdb=" N VAL B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 849 removed outlier: 3.659A pdb=" N CYS B 830 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 832 " --> pdb=" O CYS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 865 Processing helix chain 'B' and resid 866 through 888 Processing helix chain 'B' and resid 891 through 912 removed outlier: 3.636A pdb=" N VAL B 897 " --> pdb=" O TYR B 893 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 903 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET B 911 " --> pdb=" O CYS B 907 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS B 912 " --> pdb=" O LEU B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 916 Processing helix chain 'B' and resid 920 through 956 removed outlier: 3.880A pdb=" N ILE B 926 " --> pdb=" O PRO B 922 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP B 933 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 940 " --> pdb=" O PHE B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 980 removed outlier: 3.520A pdb=" N GLY B 980 " --> pdb=" O LEU B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1036 Processing helix chain 'B' and resid 1038 through 1056 removed outlier: 3.791A pdb=" N GLN B1054 " --> pdb=" O TYR B1050 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN B1056 " --> pdb=" O PHE B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1067 Processing helix chain 'B' and resid 1067 through 1077 removed outlier: 3.874A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1099 removed outlier: 3.915A pdb=" N SER B1088 " --> pdb=" O PHE B1084 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN B1091 " --> pdb=" O LEU B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1141 removed outlier: 3.719A pdb=" N ALA B1120 " --> pdb=" O ASN B1116 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU B1130 " --> pdb=" O ILE B1126 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B1131 " --> pdb=" O TYR B1127 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN B1134 " --> pdb=" O GLU B1130 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN B1135 " --> pdb=" O ASN B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1165 removed outlier: 3.657A pdb=" N ASP B1165 " --> pdb=" O LEU B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1282 removed outlier: 4.070A pdb=" N ASP B1282 " --> pdb=" O GLU B1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1279 through 1282' Processing helix chain 'B' and resid 1288 through 1292 removed outlier: 3.951A pdb=" N ASP B1291 " --> pdb=" O PRO B1288 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B1292 " --> pdb=" O MET B1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1288 through 1292' Processing helix chain 'B' and resid 1397 through 1404 Processing helix chain 'B' and resid 1410 through 1418 Processing helix chain 'B' and resid 1455 through 1463 removed outlier: 3.835A pdb=" N ARG B1459 " --> pdb=" O VAL B1455 " (cutoff:3.500A) Processing helix chain 'B' and resid 1485 through 1496 removed outlier: 3.512A pdb=" N LEU B1491 " --> pdb=" O ASN B1487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.369A pdb=" N ILE A 171 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLY A 208 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N VAL A 173 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL A 351 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS A 327 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 708 through 709 removed outlier: 3.589A pdb=" N THR A 715 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1275 through 1277 removed outlier: 3.566A pdb=" N ARG A1336 " --> pdb=" O TYR A1276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1303 through 1305 Processing sheet with id=AA6, first strand: chain 'A' and resid 1319 through 1320 Processing sheet with id=AA7, first strand: chain 'A' and resid 1385 through 1386 removed outlier: 4.055A pdb=" N LEU A1375 " --> pdb=" O VAL A1352 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL A1352 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N VAL A1377 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A1441 " --> pdb=" O ASN A1345 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP A1355 " --> pdb=" O PHE A1449 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE A1440 " --> pdb=" O TYR A1428 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR A1428 " --> pdb=" O ILE A1440 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR A1442 " --> pdb=" O LYS A1426 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS A1426 " --> pdb=" O THR A1442 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA A1444 " --> pdb=" O VAL A1424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1390 through 1391 removed outlier: 9.372A pdb=" N VAL A1377 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL A1352 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A1375 " --> pdb=" O VAL A1352 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 68 through 71 Processing sheet with id=AB1, first strand: chain 'C' and resid 128 through 130 removed outlier: 6.369A pdb=" N ILE C 171 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N GLY C 208 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N VAL C 173 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL C 351 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS C 327 " --> pdb=" O VAL C 351 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 708 through 709 removed outlier: 3.588A pdb=" N THR C 715 " --> pdb=" O SER C 709 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1275 through 1277 removed outlier: 3.566A pdb=" N ARG C1336 " --> pdb=" O TYR C1276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1303 through 1305 Processing sheet with id=AB5, first strand: chain 'C' and resid 1319 through 1320 Processing sheet with id=AB6, first strand: chain 'C' and resid 1385 through 1386 removed outlier: 4.055A pdb=" N LEU C1375 " --> pdb=" O VAL C1352 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL C1352 " --> pdb=" O LEU C1375 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N VAL C1377 " --> pdb=" O PRO C1350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C1441 " --> pdb=" O ASN C1345 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP C1355 " --> pdb=" O PHE C1449 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE C1440 " --> pdb=" O TYR C1428 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR C1428 " --> pdb=" O ILE C1440 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR C1442 " --> pdb=" O LYS C1426 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS C1426 " --> pdb=" O THR C1442 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA C1444 " --> pdb=" O VAL C1424 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1390 through 1391 removed outlier: 9.372A pdb=" N VAL C1377 " --> pdb=" O PRO C1350 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL C1352 " --> pdb=" O LEU C1375 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C1375 " --> pdb=" O VAL C1352 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 68 through 71 Processing sheet with id=AB9, first strand: chain 'D' and resid 128 through 130 removed outlier: 6.369A pdb=" N ILE D 171 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLY D 208 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL D 173 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL D 351 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS D 327 " --> pdb=" O VAL D 351 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 708 through 709 removed outlier: 3.589A pdb=" N THR D 715 " --> pdb=" O SER D 709 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1275 through 1277 removed outlier: 3.566A pdb=" N ARG D1336 " --> pdb=" O TYR D1276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1303 through 1305 Processing sheet with id=AC4, first strand: chain 'D' and resid 1319 through 1320 Processing sheet with id=AC5, first strand: chain 'D' and resid 1385 through 1386 removed outlier: 4.055A pdb=" N LEU D1375 " --> pdb=" O VAL D1352 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL D1352 " --> pdb=" O LEU D1375 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N VAL D1377 " --> pdb=" O PRO D1350 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU D1441 " --> pdb=" O ASN D1345 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP D1355 " --> pdb=" O PHE D1449 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE D1440 " --> pdb=" O TYR D1428 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR D1428 " --> pdb=" O ILE D1440 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR D1442 " --> pdb=" O LYS D1426 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS D1426 " --> pdb=" O THR D1442 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA D1444 " --> pdb=" O VAL D1424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1390 through 1391 removed outlier: 9.372A pdb=" N VAL D1377 " --> pdb=" O PRO D1350 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL D1352 " --> pdb=" O LEU D1375 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU D1375 " --> pdb=" O VAL D1352 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 68 through 71 Processing sheet with id=AC8, first strand: chain 'B' and resid 128 through 130 removed outlier: 6.369A pdb=" N ILE B 171 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLY B 208 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N VAL B 173 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL B 351 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS B 327 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 708 through 709 removed outlier: 3.589A pdb=" N THR B 715 " --> pdb=" O SER B 709 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1275 through 1277 removed outlier: 3.566A pdb=" N ARG B1336 " --> pdb=" O TYR B1276 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1303 through 1305 Processing sheet with id=AD3, first strand: chain 'B' and resid 1319 through 1320 Processing sheet with id=AD4, first strand: chain 'B' and resid 1385 through 1386 removed outlier: 4.054A pdb=" N LEU B1375 " --> pdb=" O VAL B1352 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL B1352 " --> pdb=" O LEU B1375 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N VAL B1377 " --> pdb=" O PRO B1350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B1441 " --> pdb=" O ASN B1345 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP B1355 " --> pdb=" O PHE B1449 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE B1440 " --> pdb=" O TYR B1428 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR B1428 " --> pdb=" O ILE B1440 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR B1442 " --> pdb=" O LYS B1426 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS B1426 " --> pdb=" O THR B1442 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA B1444 " --> pdb=" O VAL B1424 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1390 through 1391 removed outlier: 9.373A pdb=" N VAL B1377 " --> pdb=" O PRO B1350 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL B1352 " --> pdb=" O LEU B1375 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B1375 " --> pdb=" O VAL B1352 " (cutoff:3.500A) 1956 hydrogen bonds defined for protein. 5664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.41 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11185 1.34 - 1.45: 6856 1.45 - 1.57: 20003 1.57 - 1.69: 32 1.69 - 1.81: 204 Bond restraints: 38280 Sorted by residual: bond pdb=" N ASN B1453 " pdb=" CA ASN B1453 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.17e+01 bond pdb=" N ASN C1453 " pdb=" CA ASN C1453 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.15e+01 bond pdb=" N ASN A1453 " pdb=" CA ASN A1453 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.15e+01 bond pdb=" N ASN D1453 " pdb=" CA ASN D1453 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.15e+01 bond pdb=" N GLY B1470 " pdb=" CA GLY B1470 " ideal model delta sigma weight residual 1.444 1.480 -0.037 9.30e-03 1.16e+04 1.54e+01 ... (remaining 38275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 50445 2.53 - 5.07: 1747 5.07 - 7.60: 202 7.60 - 10.13: 70 10.13 - 12.67: 4 Bond angle restraints: 52468 Sorted by residual: angle pdb=" N PRO D 551 " pdb=" CA PRO D 551 " pdb=" CB PRO D 551 " ideal model delta sigma weight residual 103.25 110.68 -7.43 1.05e+00 9.07e-01 5.00e+01 angle pdb=" N PRO C 551 " pdb=" CA PRO C 551 " pdb=" CB PRO C 551 " ideal model delta sigma weight residual 103.25 110.66 -7.41 1.05e+00 9.07e-01 4.98e+01 angle pdb=" N PRO A 551 " pdb=" CA PRO A 551 " pdb=" CB PRO A 551 " ideal model delta sigma weight residual 103.25 110.66 -7.41 1.05e+00 9.07e-01 4.98e+01 angle pdb=" N PRO B 551 " pdb=" CA PRO B 551 " pdb=" CB PRO B 551 " ideal model delta sigma weight residual 103.25 110.66 -7.41 1.05e+00 9.07e-01 4.97e+01 angle pdb=" N ILE D1270 " pdb=" CA ILE D1270 " pdb=" C ILE D1270 " ideal model delta sigma weight residual 112.90 107.22 5.68 9.60e-01 1.09e+00 3.50e+01 ... (remaining 52463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 20173 17.20 - 34.40: 1668 34.40 - 51.60: 307 51.60 - 68.80: 108 68.80 - 86.00: 28 Dihedral angle restraints: 22284 sinusoidal: 7104 harmonic: 15180 Sorted by residual: dihedral pdb=" CA ASP B 647 " pdb=" C ASP B 647 " pdb=" N CYS B 648 " pdb=" CA CYS B 648 " ideal model delta harmonic sigma weight residual -180.00 -152.08 -27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASP A 647 " pdb=" C ASP A 647 " pdb=" N CYS A 648 " pdb=" CA CYS A 648 " ideal model delta harmonic sigma weight residual -180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA ASP C 647 " pdb=" C ASP C 647 " pdb=" N CYS C 648 " pdb=" CA CYS C 648 " ideal model delta harmonic sigma weight residual 180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 22281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4802 0.061 - 0.121: 1178 0.121 - 0.182: 199 0.182 - 0.242: 41 0.242 - 0.303: 12 Chirality restraints: 6232 Sorted by residual: chirality pdb=" CB ILE C 254 " pdb=" CA ILE C 254 " pdb=" CG1 ILE C 254 " pdb=" CG2 ILE C 254 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE A 254 " pdb=" CA ILE A 254 " pdb=" CG1 ILE A 254 " pdb=" CG2 ILE A 254 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE B 254 " pdb=" CA ILE B 254 " pdb=" CG1 ILE B 254 " pdb=" CG2 ILE B 254 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 6229 not shown) Planarity restraints: 6652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A1082 " -0.064 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO A1083 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A1083 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1083 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D1082 " 0.064 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO D1083 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO D1083 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO D1083 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B1082 " -0.064 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO B1083 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO B1083 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B1083 " -0.054 5.00e-02 4.00e+02 ... (remaining 6649 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5107 2.75 - 3.28: 37254 3.28 - 3.82: 61538 3.82 - 4.36: 66058 4.36 - 4.90: 111038 Nonbonded interactions: 280995 Sorted by model distance: nonbonded pdb=" CZ PHE A 190 " pdb=" CD2 LEU A 330 " model vdw 2.208 3.760 nonbonded pdb=" CZ PHE B 190 " pdb=" CD2 LEU B 330 " model vdw 2.208 3.760 nonbonded pdb=" CZ PHE D 190 " pdb=" CD2 LEU D 330 " model vdw 2.208 3.760 nonbonded pdb=" CZ PHE C 190 " pdb=" CD2 LEU C 330 " model vdw 2.208 3.760 nonbonded pdb=" OG SER D 146 " pdb=" OG1 THR D 149 " model vdw 2.254 3.040 ... (remaining 280990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 41.810 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 38280 Z= 0.464 Angle : 1.111 12.668 52468 Z= 0.646 Chirality : 0.058 0.303 6232 Planarity : 0.008 0.095 6652 Dihedral : 14.559 86.001 12428 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.85 % Favored : 91.61 % Rotamer: Outliers : 1.64 % Allowed : 10.84 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.10), residues: 5184 helix: -1.91 (0.08), residues: 2500 sheet: -1.81 (0.24), residues: 440 loop : -3.03 (0.11), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 250 TYR 0.021 0.002 TYR B 806 PHE 0.022 0.002 PHE D 867 TRP 0.021 0.002 TRP C 743 HIS 0.007 0.002 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00907 / 0.46 (38280) covalent geometry : angle 1.11073 / 0.65 (52468) hydrogen bonds : bond 0.19569 / 13.47 ( 1948) hydrogen bonds : angle 6.86352 / 4.93 ( 5664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9178 (mpp) cc_final: 0.8525 (mtm) REVERT: A 844 MET cc_start: 0.9009 (tpp) cc_final: 0.8664 (tmm) REVERT: A 1158 MET cc_start: 0.9349 (mmm) cc_final: 0.8971 (tpt) REVERT: C 215 MET cc_start: 0.9180 (mpp) cc_final: 0.8476 (mtm) REVERT: C 844 MET cc_start: 0.9010 (tpp) cc_final: 0.8667 (tmm) REVERT: C 1158 MET cc_start: 0.9357 (mmm) cc_final: 0.8978 (tpt) REVERT: D 215 MET cc_start: 0.9181 (mpp) cc_final: 0.8477 (mtm) REVERT: D 844 MET cc_start: 0.9011 (tpp) cc_final: 0.8663 (tmm) REVERT: D 1158 MET cc_start: 0.9359 (mmm) cc_final: 0.8979 (tpt) REVERT: B 215 MET cc_start: 0.9185 (mpp) cc_final: 0.8508 (mtm) REVERT: B 844 MET cc_start: 0.9013 (tpp) cc_final: 0.8661 (tmm) REVERT: B 1158 MET cc_start: 0.9356 (mmm) cc_final: 0.8976 (tpt) outliers start: 52 outliers final: 16 residues processed: 212 average time/residue: 0.2056 time to fit residues: 73.4217 Evaluate side-chains 156 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 394 optimal weight: 50.0000 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 0.0170 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 0.9980 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 0.7980 chunk 223 optimal weight: 6.9990 chunk 516 optimal weight: 30.0000 overall best weight: 2.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 HIS A 280 ASN A 283 HIS A 454 HIS ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN A 736 GLN A 802 ASN A1066 GLN C 280 ASN C 283 HIS C 454 HIS C 525 ASN ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN C 736 GLN C 802 ASN C1066 GLN D 283 HIS D 454 HIS D 525 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 GLN D 802 ASN D1066 GLN B 280 ASN B 283 HIS B 454 HIS B 525 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN B 736 GLN B 802 ASN B1066 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.056684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.041276 restraints weight = 277451.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.041505 restraints weight = 170609.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.041715 restraints weight = 115558.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.041855 restraints weight = 112241.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.041998 restraints weight = 99027.386| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38280 Z= 0.136 Angle : 0.607 8.089 52468 Z= 0.319 Chirality : 0.040 0.154 6232 Planarity : 0.005 0.062 6652 Dihedral : 6.183 45.092 5576 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.50 % Favored : 93.34 % Rotamer: Outliers : 1.39 % Allowed : 15.20 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.11), residues: 5184 helix: -0.26 (0.10), residues: 2616 sheet: -1.05 (0.25), residues: 388 loop : -2.71 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1254 TYR 0.012 0.001 TYR C 806 PHE 0.012 0.001 PHE C 867 TRP 0.017 0.001 TRP B 944 HIS 0.005 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (38280) covalent geometry : angle 0.60653 / 0.32 (52468) hydrogen bonds : bond 0.05255 / 3.64 ( 1948) hydrogen bonds : angle 4.84528 / 3.45 ( 5664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 VAL cc_start: 0.9469 (OUTLIER) cc_final: 0.9195 (p) REVERT: A 727 MET cc_start: 0.8533 (tpp) cc_final: 0.8108 (mmm) REVERT: A 1043 LEU cc_start: 0.8692 (tt) cc_final: 0.8488 (pp) REVERT: A 1158 MET cc_start: 0.9435 (mmm) cc_final: 0.8975 (tpt) REVERT: C 195 VAL cc_start: 0.9483 (OUTLIER) cc_final: 0.9226 (p) REVERT: C 488 MET cc_start: 0.9265 (tpp) cc_final: 0.8963 (tpp) REVERT: C 1043 LEU cc_start: 0.8713 (tt) cc_final: 0.8506 (pp) REVERT: C 1158 MET cc_start: 0.9430 (mmm) cc_final: 0.8972 (tpt) REVERT: C 1371 MET cc_start: 0.7735 (mmp) cc_final: 0.7534 (mmp) REVERT: D 195 VAL cc_start: 0.9488 (OUTLIER) cc_final: 0.9227 (p) REVERT: D 488 MET cc_start: 0.9257 (tpp) cc_final: 0.8957 (tpp) REVERT: D 1043 LEU cc_start: 0.8712 (tt) cc_final: 0.8506 (pp) REVERT: D 1158 MET cc_start: 0.9447 (mmm) cc_final: 0.8992 (tpt) REVERT: B 195 VAL cc_start: 0.9486 (OUTLIER) cc_final: 0.9213 (p) REVERT: B 488 MET cc_start: 0.9249 (tpp) cc_final: 0.8944 (tpp) REVERT: B 1043 LEU cc_start: 0.8709 (tt) cc_final: 0.8503 (pp) REVERT: B 1158 MET cc_start: 0.9418 (mmm) cc_final: 0.9008 (tpt) outliers start: 44 outliers final: 18 residues processed: 210 average time/residue: 0.1885 time to fit residues: 70.0573 Evaluate side-chains 172 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 883 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 434 optimal weight: 10.0000 chunk 242 optimal weight: 40.0000 chunk 155 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 466 optimal weight: 7.9990 chunk 449 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1437 ASN A1476 GLN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 633 ASN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1437 ASN C1476 GLN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 633 ASN D 719 GLN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1437 ASN D1476 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 ASN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1437 ASN B1476 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.055450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.040139 restraints weight = 280918.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.040263 restraints weight = 171188.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.040308 restraints weight = 129424.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.040536 restraints weight = 121350.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.040610 restraints weight = 107851.091| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 38280 Z= 0.244 Angle : 0.652 7.585 52468 Z= 0.337 Chirality : 0.041 0.137 6232 Planarity : 0.005 0.053 6652 Dihedral : 5.726 46.732 5552 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.04 % Favored : 91.80 % Rotamer: Outliers : 3.12 % Allowed : 17.21 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.12), residues: 5184 helix: 0.54 (0.10), residues: 2616 sheet: -1.24 (0.25), residues: 408 loop : -2.53 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 302 TYR 0.014 0.001 TYR B 806 PHE 0.015 0.001 PHE C 690 TRP 0.013 0.001 TRP A 944 HIS 0.004 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (38280) covalent geometry : angle 0.65232 / 0.34 (52468) hydrogen bonds : bond 0.05086 / 3.51 ( 1948) hydrogen bonds : angle 4.82660 / 3.44 ( 5664) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 140 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.8277 (m-10) REVERT: A 633 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8751 (t0) REVERT: A 747 LEU cc_start: 0.9781 (OUTLIER) cc_final: 0.9485 (pp) REVERT: A 844 MET cc_start: 0.8975 (ttp) cc_final: 0.8724 (ptt) REVERT: A 1158 MET cc_start: 0.9445 (mmm) cc_final: 0.9016 (tpt) REVERT: C 295 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.8281 (m-10) REVERT: C 522 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9495 (mm) REVERT: C 633 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8758 (t0) REVERT: C 747 LEU cc_start: 0.9778 (OUTLIER) cc_final: 0.9483 (pp) REVERT: C 844 MET cc_start: 0.8979 (ttp) cc_final: 0.8732 (ptt) REVERT: C 1158 MET cc_start: 0.9444 (mmm) cc_final: 0.9131 (mmm) REVERT: D 295 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8273 (m-10) REVERT: D 633 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8764 (t0) REVERT: D 747 LEU cc_start: 0.9776 (OUTLIER) cc_final: 0.9476 (pp) REVERT: D 844 MET cc_start: 0.8988 (ttp) cc_final: 0.8738 (ptt) REVERT: D 1158 MET cc_start: 0.9448 (mmm) cc_final: 0.9085 (mmm) REVERT: B 295 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.8282 (m-10) REVERT: B 522 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9483 (mm) REVERT: B 633 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8760 (t0) REVERT: B 747 LEU cc_start: 0.9776 (OUTLIER) cc_final: 0.9479 (pp) REVERT: B 1158 MET cc_start: 0.9410 (mmm) cc_final: 0.9067 (tpt) outliers start: 99 outliers final: 51 residues processed: 225 average time/residue: 0.2045 time to fit residues: 81.5162 Evaluate side-chains 205 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 140 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1311 ARG Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 841 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1311 ARG Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 633 ASN Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 841 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1311 ARG Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 633 ASN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 841 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1311 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 438 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 330 optimal weight: 10.0000 chunk 350 optimal weight: 20.0000 chunk 394 optimal weight: 30.0000 chunk 319 optimal weight: 8.9990 chunk 344 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.055863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.040435 restraints weight = 278121.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.040682 restraints weight = 171863.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.040766 restraints weight = 121626.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.041000 restraints weight = 115856.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.041102 restraints weight = 101870.637| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 38280 Z= 0.177 Angle : 0.576 5.801 52468 Z= 0.298 Chirality : 0.040 0.134 6232 Planarity : 0.005 0.052 6652 Dihedral : 5.408 46.379 5548 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.10 % Favored : 92.75 % Rotamer: Outliers : 4.10 % Allowed : 16.87 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.12), residues: 5184 helix: 0.89 (0.10), residues: 2620 sheet: -1.32 (0.24), residues: 440 loop : -2.46 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 635 TYR 0.012 0.001 TYR B 806 PHE 0.012 0.001 PHE C 690 TRP 0.013 0.001 TRP A 944 HIS 0.003 0.001 HIS C1502 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (38280) covalent geometry : angle 0.57612 / 0.30 (52468) hydrogen bonds : bond 0.04518 / 3.12 ( 1948) hydrogen bonds : angle 4.54532 / 3.24 ( 5664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 142 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8208 (m-10) REVERT: A 747 LEU cc_start: 0.9775 (OUTLIER) cc_final: 0.9468 (pp) REVERT: A 1043 LEU cc_start: 0.8807 (tt) cc_final: 0.8496 (pp) REVERT: A 1158 MET cc_start: 0.9438 (mmm) cc_final: 0.9108 (mmm) REVERT: C 295 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.8138 (m-10) REVERT: C 747 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9467 (pp) REVERT: C 1043 LEU cc_start: 0.8793 (tt) cc_final: 0.8484 (pp) REVERT: C 1158 MET cc_start: 0.9430 (mmm) cc_final: 0.9088 (mmm) REVERT: D 295 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8126 (m-10) REVERT: D 747 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9466 (pp) REVERT: D 1043 LEU cc_start: 0.8794 (tt) cc_final: 0.8487 (pp) REVERT: D 1158 MET cc_start: 0.9434 (mmm) cc_final: 0.9082 (mmm) REVERT: B 295 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8131 (m-10) REVERT: B 522 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9484 (mm) REVERT: B 747 LEU cc_start: 0.9771 (OUTLIER) cc_final: 0.9464 (pp) REVERT: B 1043 LEU cc_start: 0.8794 (tt) cc_final: 0.8485 (pp) REVERT: B 1158 MET cc_start: 0.9409 (mmm) cc_final: 0.9105 (mmm) outliers start: 130 outliers final: 81 residues processed: 262 average time/residue: 0.2020 time to fit residues: 94.1871 Evaluate side-chains 232 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 142 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1311 ARG Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1311 ARG Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 816 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1311 ARG Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 841 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1311 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 323 optimal weight: 8.9990 chunk 503 optimal weight: 4.9990 chunk 287 optimal weight: 7.9990 chunk 475 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 chunk 444 optimal weight: 2.9990 chunk 252 optimal weight: 0.9990 chunk 474 optimal weight: 7.9990 chunk 394 optimal weight: 30.0000 chunk 183 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.056588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.041338 restraints weight = 277572.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.041413 restraints weight = 168704.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.041542 restraints weight = 120436.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.041720 restraints weight = 114308.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.041860 restraints weight = 101268.711| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38280 Z= 0.118 Angle : 0.542 8.825 52468 Z= 0.275 Chirality : 0.039 0.139 6232 Planarity : 0.004 0.054 6652 Dihedral : 5.048 45.858 5544 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.16 % Favored : 92.77 % Rotamer: Outliers : 3.78 % Allowed : 17.81 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.12), residues: 5184 helix: 1.24 (0.10), residues: 2624 sheet: -1.20 (0.23), residues: 432 loop : -2.38 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 411 TYR 0.011 0.001 TYR B 806 PHE 0.011 0.001 PHE A 867 TRP 0.011 0.001 TRP A 944 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (38280) covalent geometry : angle 0.54160 / 0.28 (52468) hydrogen bonds : bond 0.03911 / 2.71 ( 1948) hydrogen bonds : angle 4.21433 / 3.00 ( 5664) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 148 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.8094 (m-10) REVERT: A 747 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9445 (pp) REVERT: A 844 MET cc_start: 0.9059 (ttp) cc_final: 0.8722 (ptt) REVERT: A 1158 MET cc_start: 0.9437 (mmm) cc_final: 0.9099 (mmm) REVERT: C 295 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8098 (m-10) REVERT: C 747 LEU cc_start: 0.9754 (OUTLIER) cc_final: 0.9446 (pp) REVERT: C 844 MET cc_start: 0.9064 (ttp) cc_final: 0.8729 (ptt) REVERT: C 931 MET cc_start: 0.6533 (tmm) cc_final: 0.6277 (tmm) REVERT: C 1158 MET cc_start: 0.9437 (mmm) cc_final: 0.9035 (mmm) REVERT: C 1502 HIS cc_start: 0.7061 (OUTLIER) cc_final: 0.6112 (p90) REVERT: D 295 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.8094 (m-10) REVERT: D 747 LEU cc_start: 0.9759 (OUTLIER) cc_final: 0.9456 (pp) REVERT: D 844 MET cc_start: 0.9067 (ttp) cc_final: 0.8729 (ptt) REVERT: D 931 MET cc_start: 0.6527 (tmm) cc_final: 0.6273 (tmm) REVERT: D 1158 MET cc_start: 0.9439 (mmm) cc_final: 0.9053 (tpt) REVERT: B 295 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8084 (m-10) REVERT: B 747 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9461 (pp) REVERT: B 844 MET cc_start: 0.9056 (ttp) cc_final: 0.8790 (ptt) REVERT: B 1158 MET cc_start: 0.9405 (mmm) cc_final: 0.9086 (mmm) outliers start: 120 outliers final: 76 residues processed: 250 average time/residue: 0.1928 time to fit residues: 87.9716 Evaluate side-chains 229 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 144 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 830 CYS Chi-restraints excluded: chain C residue 841 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 LEU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1371 MET Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 830 CYS Chi-restraints excluded: chain D residue 841 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 841 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1351 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 139 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 475 optimal weight: 10.0000 chunk 512 optimal weight: 9.9990 chunk 248 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 498 optimal weight: 20.0000 chunk 206 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 HIS ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.055372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.039954 restraints weight = 280742.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.040257 restraints weight = 167068.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.040192 restraints weight = 127611.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.040468 restraints weight = 120441.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.040518 restraints weight = 105541.870| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 38280 Z= 0.252 Angle : 0.645 8.176 52468 Z= 0.327 Chirality : 0.041 0.139 6232 Planarity : 0.005 0.048 6652 Dihedral : 5.149 47.918 5544 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.95 % Favored : 91.98 % Rotamer: Outliers : 4.19 % Allowed : 17.56 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.12), residues: 5184 helix: 1.23 (0.10), residues: 2628 sheet: -1.27 (0.23), residues: 432 loop : -2.41 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1311 TYR 0.011 0.001 TYR D 806 PHE 0.015 0.002 PHE A 690 TRP 0.013 0.001 TRP D1385 HIS 0.005 0.001 HIS A1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.25 (38280) covalent geometry : angle 0.64467 / 0.33 (52468) hydrogen bonds : bond 0.04610 / 3.19 ( 1948) hydrogen bonds : angle 4.57495 / 3.26 ( 5664) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 140 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.8299 (m-10) REVERT: A 747 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9459 (pp) REVERT: A 844 MET cc_start: 0.9071 (ttp) cc_final: 0.8778 (ptt) REVERT: A 931 MET cc_start: 0.6577 (tmm) cc_final: 0.6374 (tmm) REVERT: A 1158 MET cc_start: 0.9447 (mmm) cc_final: 0.9111 (mmm) REVERT: A 1502 HIS cc_start: 0.7210 (OUTLIER) cc_final: 0.6092 (p90) REVERT: C 295 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8284 (m-10) REVERT: C 747 LEU cc_start: 0.9775 (OUTLIER) cc_final: 0.9460 (pp) REVERT: C 844 MET cc_start: 0.9072 (ttp) cc_final: 0.8784 (ptt) REVERT: C 931 MET cc_start: 0.6664 (tmm) cc_final: 0.6437 (tmm) REVERT: C 1158 MET cc_start: 0.9453 (mmm) cc_final: 0.9073 (tpt) REVERT: C 1371 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7171 (mmp) REVERT: C 1502 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.6220 (p90) REVERT: D 295 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8281 (m-10) REVERT: D 747 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9458 (pp) REVERT: D 844 MET cc_start: 0.9077 (ttp) cc_final: 0.8786 (ptt) REVERT: D 931 MET cc_start: 0.6663 (tmm) cc_final: 0.6435 (tmm) REVERT: D 1158 MET cc_start: 0.9465 (mmm) cc_final: 0.9127 (tpt) REVERT: B 295 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8293 (m-10) REVERT: B 522 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9493 (mm) REVERT: B 747 LEU cc_start: 0.9775 (OUTLIER) cc_final: 0.9458 (pp) REVERT: B 844 MET cc_start: 0.9071 (ttp) cc_final: 0.8798 (ptt) REVERT: B 931 MET cc_start: 0.6458 (tmm) cc_final: 0.6238 (tmm) REVERT: B 1158 MET cc_start: 0.9432 (mmm) cc_final: 0.9082 (mmm) outliers start: 133 outliers final: 89 residues processed: 256 average time/residue: 0.1935 time to fit residues: 88.6337 Evaluate side-chains 241 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 140 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1311 ARG Chi-restraints excluded: chain A residue 1351 MET Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 830 CYS Chi-restraints excluded: chain C residue 841 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1311 ARG Chi-restraints excluded: chain C residue 1351 MET Chi-restraints excluded: chain C residue 1371 MET Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 830 CYS Chi-restraints excluded: chain D residue 841 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1311 ARG Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1311 ARG Chi-restraints excluded: chain B residue 1351 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 423 optimal weight: 8.9990 chunk 418 optimal weight: 7.9990 chunk 348 optimal weight: 50.0000 chunk 156 optimal weight: 0.0070 chunk 165 optimal weight: 1.9990 chunk 233 optimal weight: 20.0000 chunk 249 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 294 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 444 optimal weight: 1.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.056335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.041039 restraints weight = 278730.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.041320 restraints weight = 166694.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.041283 restraints weight = 125597.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.041558 restraints weight = 118111.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.041617 restraints weight = 104115.788| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38280 Z= 0.126 Angle : 0.551 10.050 52468 Z= 0.279 Chirality : 0.039 0.233 6232 Planarity : 0.004 0.053 6652 Dihedral : 4.907 46.218 5544 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer: Outliers : 3.85 % Allowed : 17.50 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.12), residues: 5184 helix: 1.55 (0.11), residues: 2628 sheet: -1.19 (0.24), residues: 432 loop : -2.30 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 411 TYR 0.010 0.001 TYR D 806 PHE 0.016 0.001 PHE C1035 TRP 0.012 0.001 TRP A 944 HIS 0.004 0.001 HIS D1089 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (38280) covalent geometry : angle 0.55138 / 0.28 (52468) hydrogen bonds : bond 0.03936 / 2.72 ( 1948) hydrogen bonds : angle 4.15313 / 2.96 ( 5664) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 138 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8105 (m-10) REVERT: A 747 LEU cc_start: 0.9764 (OUTLIER) cc_final: 0.9449 (pp) REVERT: A 844 MET cc_start: 0.9117 (ttp) cc_final: 0.8811 (ptt) REVERT: A 931 MET cc_start: 0.6592 (tmm) cc_final: 0.6344 (tmm) REVERT: A 1043 LEU cc_start: 0.8802 (tt) cc_final: 0.8456 (pp) REVERT: A 1158 MET cc_start: 0.9443 (mmm) cc_final: 0.9097 (mmm) REVERT: A 1502 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6116 (p90) REVERT: C 295 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.8094 (m-10) REVERT: C 747 LEU cc_start: 0.9764 (OUTLIER) cc_final: 0.9449 (pp) REVERT: C 844 MET cc_start: 0.9122 (ttp) cc_final: 0.8822 (ptt) REVERT: C 1043 LEU cc_start: 0.8795 (tt) cc_final: 0.8453 (pp) REVERT: C 1158 MET cc_start: 0.9444 (mmm) cc_final: 0.9023 (tpt) REVERT: C 1371 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7199 (mmp) REVERT: C 1502 HIS cc_start: 0.7256 (OUTLIER) cc_final: 0.6286 (p90) REVERT: D 295 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.8100 (m-10) REVERT: D 747 LEU cc_start: 0.9765 (OUTLIER) cc_final: 0.9451 (pp) REVERT: D 844 MET cc_start: 0.9138 (ttp) cc_final: 0.8853 (ptt) REVERT: D 1043 LEU cc_start: 0.8793 (tt) cc_final: 0.8454 (pp) REVERT: D 1158 MET cc_start: 0.9459 (mmm) cc_final: 0.9107 (tpt) REVERT: D 1371 MET cc_start: 0.7926 (mmt) cc_final: 0.7353 (mmp) REVERT: D 1502 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6238 (p90) REVERT: B 295 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8098 (m-10) REVERT: B 747 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9452 (pp) REVERT: B 844 MET cc_start: 0.9145 (ttp) cc_final: 0.8854 (ptt) REVERT: B 931 MET cc_start: 0.6508 (tmm) cc_final: 0.6235 (tmm) REVERT: B 1043 LEU cc_start: 0.8792 (tt) cc_final: 0.8447 (pp) REVERT: B 1158 MET cc_start: 0.9419 (mmm) cc_final: 0.9047 (mmm) REVERT: B 1502 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.6212 (p90) outliers start: 122 outliers final: 89 residues processed: 251 average time/residue: 0.1969 time to fit residues: 88.2636 Evaluate side-chains 240 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 138 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1311 ARG Chi-restraints excluded: chain A residue 1351 MET Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 830 CYS Chi-restraints excluded: chain C residue 841 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1311 ARG Chi-restraints excluded: chain C residue 1351 MET Chi-restraints excluded: chain C residue 1371 MET Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 830 CYS Chi-restraints excluded: chain D residue 841 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1159 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1311 ARG Chi-restraints excluded: chain D residue 1351 MET Chi-restraints excluded: chain D residue 1502 HIS Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1311 ARG Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1502 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 446 optimal weight: 4.9990 chunk 332 optimal weight: 10.0000 chunk 459 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 401 optimal weight: 3.9990 chunk 222 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 chunk 429 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 288 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1089 HIS ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1089 HIS ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.055587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.040494 restraints weight = 268293.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.040257 restraints weight = 158978.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.040519 restraints weight = 127671.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.040552 restraints weight = 122940.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.040626 restraints weight = 107037.081| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38280 Z= 0.162 Angle : 0.563 9.520 52468 Z= 0.285 Chirality : 0.040 0.206 6232 Planarity : 0.004 0.052 6652 Dihedral : 4.869 45.827 5544 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 4.22 % Allowed : 17.50 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.12), residues: 5184 helix: 1.63 (0.11), residues: 2616 sheet: -1.22 (0.23), residues: 432 loop : -2.25 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 886 TYR 0.010 0.001 TYR A1074 PHE 0.013 0.001 PHE C1035 TRP 0.011 0.001 TRP C 944 HIS 0.006 0.001 HIS D1089 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (38280) covalent geometry : angle 0.56255 / 0.29 (52468) hydrogen bonds : bond 0.03948 / 2.73 ( 1948) hydrogen bonds : angle 4.17435 / 2.98 ( 5664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 138 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.8042 (m-10) REVERT: A 747 LEU cc_start: 0.9764 (OUTLIER) cc_final: 0.9448 (pp) REVERT: A 844 MET cc_start: 0.9107 (ttp) cc_final: 0.8906 (ptt) REVERT: A 1043 LEU cc_start: 0.8831 (tt) cc_final: 0.8478 (pp) REVERT: A 1089 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7742 (m-70) REVERT: A 1158 MET cc_start: 0.9445 (mmm) cc_final: 0.9097 (mmm) REVERT: A 1502 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6218 (p90) REVERT: C 295 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8010 (m-10) REVERT: C 747 LEU cc_start: 0.9763 (OUTLIER) cc_final: 0.9447 (pp) REVERT: C 844 MET cc_start: 0.9140 (ttp) cc_final: 0.8927 (ptt) REVERT: C 1043 LEU cc_start: 0.8822 (tt) cc_final: 0.8471 (pp) REVERT: C 1089 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7755 (m-70) REVERT: C 1158 MET cc_start: 0.9451 (mmm) cc_final: 0.9026 (tpt) REVERT: C 1371 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7227 (mmp) REVERT: C 1502 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6279 (p90) REVERT: D 295 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.8013 (m-10) REVERT: D 747 LEU cc_start: 0.9768 (OUTLIER) cc_final: 0.9464 (pp) REVERT: D 844 MET cc_start: 0.9142 (ttp) cc_final: 0.8927 (ptt) REVERT: D 1043 LEU cc_start: 0.8822 (tt) cc_final: 0.8472 (pp) REVERT: D 1089 HIS cc_start: 0.8096 (OUTLIER) cc_final: 0.7752 (m-70) REVERT: D 1158 MET cc_start: 0.9461 (mmm) cc_final: 0.9107 (tpt) REVERT: D 1371 MET cc_start: 0.7929 (mmt) cc_final: 0.7311 (mmp) REVERT: D 1502 HIS cc_start: 0.7236 (OUTLIER) cc_final: 0.6272 (p90) REVERT: B 295 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8010 (m-10) REVERT: B 747 LEU cc_start: 0.9771 (OUTLIER) cc_final: 0.9466 (pp) REVERT: B 930 MET cc_start: 0.9336 (mmm) cc_final: 0.9112 (mmp) REVERT: B 1043 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8470 (pp) REVERT: B 1089 HIS cc_start: 0.8157 (OUTLIER) cc_final: 0.7913 (m-70) REVERT: B 1158 MET cc_start: 0.9428 (mmm) cc_final: 0.9055 (mmm) REVERT: B 1502 HIS cc_start: 0.7225 (OUTLIER) cc_final: 0.6242 (p90) outliers start: 134 outliers final: 101 residues processed: 258 average time/residue: 0.2011 time to fit residues: 92.1823 Evaluate side-chains 257 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 138 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1089 HIS Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1311 ARG Chi-restraints excluded: chain A residue 1351 MET Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 830 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1089 HIS Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1311 ARG Chi-restraints excluded: chain C residue 1351 MET Chi-restraints excluded: chain C residue 1371 MET Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 830 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1089 HIS Chi-restraints excluded: chain D residue 1159 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1311 ARG Chi-restraints excluded: chain D residue 1351 MET Chi-restraints excluded: chain D residue 1502 HIS Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1089 HIS Chi-restraints excluded: chain B residue 1159 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1311 ARG Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1502 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 406 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 238 optimal weight: 3.9990 chunk 418 optimal weight: 6.9990 chunk 277 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 486 optimal weight: 0.9980 chunk 378 optimal weight: 30.0000 chunk 74 optimal weight: 6.9990 chunk 388 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1089 HIS ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1089 HIS ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.056157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.040871 restraints weight = 280033.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.041344 restraints weight = 166978.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.041267 restraints weight = 125325.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.041475 restraints weight = 115512.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.041542 restraints weight = 107069.348| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 38280 Z= 0.158 Angle : 0.561 9.689 52468 Z= 0.284 Chirality : 0.040 0.205 6232 Planarity : 0.004 0.052 6652 Dihedral : 4.836 45.383 5544 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 4.19 % Allowed : 17.84 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 5184 helix: 1.68 (0.11), residues: 2616 sheet: -1.21 (0.23), residues: 432 loop : -2.22 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 886 TYR 0.009 0.001 TYR B 806 PHE 0.016 0.001 PHE C1035 TRP 0.015 0.001 TRP B 944 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (38280) covalent geometry : angle 0.56137 / 0.28 (52468) hydrogen bonds : bond 0.03897 / 2.70 ( 1948) hydrogen bonds : angle 4.14139 / 2.96 ( 5664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 138 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8051 (m-10) REVERT: A 747 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9466 (pp) REVERT: A 844 MET cc_start: 0.9146 (ttp) cc_final: 0.8836 (ptt) REVERT: A 1043 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8426 (pp) REVERT: A 1158 MET cc_start: 0.9447 (mmm) cc_final: 0.9102 (mmm) REVERT: A 1502 HIS cc_start: 0.7187 (OUTLIER) cc_final: 0.6216 (p90) REVERT: C 295 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8026 (m-10) REVERT: C 747 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9468 (pp) REVERT: C 844 MET cc_start: 0.9149 (ttp) cc_final: 0.8844 (ptt) REVERT: C 1043 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8431 (pp) REVERT: C 1158 MET cc_start: 0.9450 (mmm) cc_final: 0.9029 (tpt) REVERT: C 1371 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7232 (mmp) REVERT: C 1502 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6307 (p90) REVERT: D 295 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8027 (m-10) REVERT: D 747 LEU cc_start: 0.9775 (OUTLIER) cc_final: 0.9472 (pp) REVERT: D 844 MET cc_start: 0.9152 (ttp) cc_final: 0.8843 (ptt) REVERT: D 1043 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8428 (pp) REVERT: D 1158 MET cc_start: 0.9464 (mmm) cc_final: 0.9114 (tpt) REVERT: D 1371 MET cc_start: 0.7918 (mmt) cc_final: 0.7324 (mmp) REVERT: D 1502 HIS cc_start: 0.7230 (OUTLIER) cc_final: 0.6311 (p90) REVERT: B 295 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8033 (m-10) REVERT: B 747 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9471 (pp) REVERT: B 844 MET cc_start: 0.9202 (ttp) cc_final: 0.8918 (ptt) REVERT: B 930 MET cc_start: 0.9324 (mmm) cc_final: 0.9083 (mmp) REVERT: B 1043 LEU cc_start: 0.8792 (tt) cc_final: 0.8561 (pp) REVERT: B 1158 MET cc_start: 0.9424 (mmm) cc_final: 0.9051 (mmm) REVERT: B 1371 MET cc_start: 0.7899 (mmt) cc_final: 0.7116 (mmp) REVERT: B 1502 HIS cc_start: 0.7217 (OUTLIER) cc_final: 0.6090 (p90) outliers start: 133 outliers final: 103 residues processed: 255 average time/residue: 0.1959 time to fit residues: 89.1901 Evaluate side-chains 257 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 138 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1089 HIS Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1311 ARG Chi-restraints excluded: chain A residue 1351 MET Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 830 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 LEU Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1089 HIS Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1311 ARG Chi-restraints excluded: chain C residue 1351 MET Chi-restraints excluded: chain C residue 1371 MET Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 830 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1089 HIS Chi-restraints excluded: chain D residue 1159 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1311 ARG Chi-restraints excluded: chain D residue 1351 MET Chi-restraints excluded: chain D residue 1502 HIS Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1089 HIS Chi-restraints excluded: chain B residue 1159 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1311 ARG Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1502 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 302 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 265 optimal weight: 0.5980 chunk 380 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 2 optimal weight: 50.0000 chunk 501 optimal weight: 40.0000 chunk 467 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1089 HIS ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1089 HIS ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.056707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041710 restraints weight = 276837.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.042218 restraints weight = 150491.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.042303 restraints weight = 105930.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.042464 restraints weight = 100651.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.042541 restraints weight = 91279.187| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 38280 Z= 0.106 Angle : 0.542 10.245 52468 Z= 0.273 Chirality : 0.039 0.209 6232 Planarity : 0.004 0.053 6652 Dihedral : 4.735 44.213 5544 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 3.53 % Allowed : 18.44 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.12), residues: 5184 helix: 1.75 (0.11), residues: 2624 sheet: -1.11 (0.24), residues: 432 loop : -2.18 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 845 TYR 0.009 0.001 TYR A1074 PHE 0.014 0.001 PHE B1035 TRP 0.015 0.001 TRP C 944 HIS 0.011 0.001 HIS B1089 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (38280) covalent geometry : angle 0.54215 / 0.27 (52468) hydrogen bonds : bond 0.03634 / 2.52 ( 1948) hydrogen bonds : angle 3.99465 / 2.85 ( 5664) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 138 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: A 747 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9442 (pp) REVERT: A 844 MET cc_start: 0.9147 (ttp) cc_final: 0.8832 (ptt) REVERT: A 1035 PHE cc_start: 0.7580 (t80) cc_final: 0.7349 (t80) REVERT: A 1043 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8366 (pp) REVERT: A 1158 MET cc_start: 0.9439 (mmm) cc_final: 0.9078 (mmm) REVERT: A 1502 HIS cc_start: 0.7153 (OUTLIER) cc_final: 0.6245 (p90) REVERT: C 295 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7933 (m-10) REVERT: C 747 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9442 (pp) REVERT: C 844 MET cc_start: 0.9205 (ttp) cc_final: 0.8853 (ptt) REVERT: C 1035 PHE cc_start: 0.7632 (t80) cc_final: 0.7393 (t80) REVERT: C 1043 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8371 (pp) REVERT: C 1158 MET cc_start: 0.9441 (mmm) cc_final: 0.8997 (tpt) REVERT: C 1371 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7189 (mmp) REVERT: C 1502 HIS cc_start: 0.7182 (OUTLIER) cc_final: 0.6288 (p90) REVERT: D 295 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7933 (m-10) REVERT: D 747 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9449 (pp) REVERT: D 844 MET cc_start: 0.9206 (ttp) cc_final: 0.8850 (ptt) REVERT: D 1035 PHE cc_start: 0.7636 (t80) cc_final: 0.7399 (t80) REVERT: D 1043 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8374 (pp) REVERT: D 1158 MET cc_start: 0.9453 (mmm) cc_final: 0.9059 (tpt) REVERT: D 1371 MET cc_start: 0.7907 (mmt) cc_final: 0.7146 (mmp) REVERT: D 1502 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.6058 (p90) REVERT: B 295 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7941 (m-10) REVERT: B 747 LEU cc_start: 0.9742 (OUTLIER) cc_final: 0.9448 (pp) REVERT: B 844 MET cc_start: 0.9153 (ttp) cc_final: 0.8900 (ptt) REVERT: B 930 MET cc_start: 0.9280 (mmm) cc_final: 0.9013 (mmp) REVERT: B 1035 PHE cc_start: 0.7627 (t80) cc_final: 0.7415 (t80) REVERT: B 1043 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8355 (pp) REVERT: B 1158 MET cc_start: 0.9415 (mmm) cc_final: 0.9028 (mmm) REVERT: B 1371 MET cc_start: 0.7871 (mmt) cc_final: 0.7099 (mmp) REVERT: B 1502 HIS cc_start: 0.7162 (OUTLIER) cc_final: 0.6053 (p90) outliers start: 112 outliers final: 92 residues processed: 236 average time/residue: 0.1955 time to fit residues: 82.3157 Evaluate side-chains 247 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 138 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1089 HIS Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1351 MET Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 830 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 LEU Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1089 HIS Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1311 ARG Chi-restraints excluded: chain C residue 1351 MET Chi-restraints excluded: chain C residue 1371 MET Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 830 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1089 HIS Chi-restraints excluded: chain D residue 1159 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1311 ARG Chi-restraints excluded: chain D residue 1351 MET Chi-restraints excluded: chain D residue 1502 HIS Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1089 HIS Chi-restraints excluded: chain B residue 1159 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1502 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 404 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 369 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 294 optimal weight: 4.9990 chunk 335 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1089 HIS ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1089 HIS ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.056639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.041562 restraints weight = 278775.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.041930 restraints weight = 161039.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.041970 restraints weight = 117017.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.042082 restraints weight = 116418.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.042289 restraints weight = 101882.668| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38280 Z= 0.118 Angle : 0.542 10.163 52468 Z= 0.272 Chirality : 0.039 0.206 6232 Planarity : 0.004 0.053 6652 Dihedral : 4.685 43.547 5544 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.40 % Favored : 93.52 % Rotamer: Outliers : 3.72 % Allowed : 18.22 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.12), residues: 5184 helix: 1.80 (0.11), residues: 2624 sheet: -1.10 (0.24), residues: 432 loop : -2.17 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 886 TYR 0.009 0.001 TYR C1074 PHE 0.013 0.001 PHE B1035 TRP 0.014 0.001 TRP B 944 HIS 0.009 0.001 HIS B1089 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (38280) covalent geometry : angle 0.54235 / 0.27 (52468) hydrogen bonds : bond 0.03558 / 2.46 ( 1948) hydrogen bonds : angle 3.97642 / 2.84 ( 5664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5437.55 seconds wall clock time: 95 minutes 9.06 seconds (5709.06 seconds total)